Just checked back through old versions of the CNS/XPLOR forcefield and it
has always been so. I guess this is partly historical - NMR structures
were typically recorded at lower pH if they could be - and partly a good
default setting as electrostatics didn't used to be used for refinement.
Even if you set a different (partial?) protonation state in analysis, I
would be surprised if ARIA paid attention to what you'd done if the
residue code was still HIS in the sequence though. Looks as if the data
model is intended to deal with protonation state via "chain state"s rather
than alternative residue types.
If you know that your HIS are likely to be singly protonated (experimental
evidence, pH, etc.) and can either determine or want to take a punt on
which N is protonated then you should use the HISD or HISE patches in your
ARIA setup.
I reckon that you are right that it would be nice to be able to set your
experimental pH, per residue pKas, and have CNS/ARIA cope with that,
because as you say it will likely have an impact on the water refinement
stage. Probably not a high priority in the grand scheme of things though!
Brian Smith
--
Dr. Brian O. Smith ---------------------- Brian Smith at glasgow ac uk
School of Life Sciences, College of Medical, Vetinary & Life Sciences,
Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
Tel: 0141 330 5167/6459/3089 Fax: 0141 330 4600
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